SAN PABLO -- Following months of bitter custody battles and claims of physical abuse, a Richmond mother killed her estranged husband and abducted their three children, prompting a brief statewide Amber Alert on Monday night, according to police and court records.

The children, ages 3, 6 and 12, were found safe in the 400 block of South 8th Street in Richmond around 11:30 p.m. Monday. Their mother, 35-year-old Alicia Ortez, and a male companion were arrested on suspicion of shooting to death Oscar Anguiano, 32.

Ortez was being held on $1 million bail Tuesday at the County Jail in Martinez. Police had still not released the male companion's identity, charges or bail status as of Tuesday afternoon.

Police found Anguiano inside or near a small outbuilding in the backyard of a house on the 1600 block of 16th Street in San Pablo around 8 a.m. Monday, according to San Pablo police Cmdr. Jeff Palmieri. His three children were not at the house when police discovered his body; they had recently begun living solely with Anguiano after he told a judge that Ortez had not been picking them up at scheduled meetings.

California Highway Patrol officials issued an Amber Alert for the missing children about 12 hours later.

A resident of the home had discovered the body and contacted police, Palmieri said, and a neighbor said gunshots were heard in the area around midnight Monday.

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Palmieri said investigators developed leads that led them to the San Pablo address and eventually to the home in Richmond where the children were found. The California Highway Patrol canceled the Amber Alert at 1 a.m.

Police did not say where the children were taken after police found them, but Palmieri said they're "in a safe place."

"We are making sure their needs are being met," he said. "That includes whatever emotional or mental health help that they may need."

Contra Costa court records show a strained relationship between the estranged couple.

In November, Ortez was granted a temporary restraining order against Anguiano, claiming he physically abused her since 2002 and that she had marks on her body to prove it. She detailed what she claimed was the most recent abuse incident on Nov. 17:

"Respondent was very angry and hit me on my head and threw me to the floor," Ortez wrote in court papers. "This person has constantly abused me since 2002. I fear for my life, I do not want this person near me. I am very scared, this person mentioned to me that he had a gun. He has threatened to kill me in the past."

She said police had responded to domestic violence incidents in the past, including a 2006 encounter in Richmond. She also claimed he had a gun, according to the petition.

A judge briefly took visitation rights away from Anguiano.

By December, Judge Christopher Bowen awarded joint custody to Anguiano and extended the restraining order, but ordered the father to remain in the car when picking up and dropping off the kids, according to court documents.

Anguiano was allowed "brief and peaceful contact with mother regarding visitation of the children, but mother has expressed that she wishes for father not to contact her at all," according to court minutes.

Before the next hearing, Ortez filed a declaration saying her husband had only picked the kids up once, and had not paid rent or child expenses.

In early February, the couple's landlord at a house on 22nd Street in Richmond sued them for not paying the previous month's rent and threatened to evict them, although court records show only Ortez was living there with her kids.

Later that month, Bowen again extended the restraining order until May 15, despite Anguiano's objections, and modified the split custody of the children. The judge ordered therapy for the mother and kids and a child support review, according to court documents.

On April 1, Anguiano petitioned the court for temporary emergency custody of the kids with no visitation to his wife, saying Ortez had briefly moved into a hotel, but her new residence was unknown and she was not watching her kids.

"I need to get sole legal and physical (custody) because I cannot depend on her to take care of the children," Anguiano wrote. "I am going to arrange for child care so I can get to work on time and support my family ... If they are going to be with me all the time I need to get a bigger place."

The couple, who represented themselves during their court battles, failed to appear at the last hearing May 15. Judge Bowen kept the custody agreement in effect, but ended the restraining order.

Ortez and Anguiano were scheduled to next appear July 1.

Staff writer David DeBolt contributed to this story. Contact Matthias Gafni at 925-952-5026 and follow him at Twitter.com/mgafni.